Streptococcus pneumoniae (S. pneumoniae) is the chief cause of community-acquired pneumonia (CAP). S. pneumoniae is a Gram-positive bacteria responsible for considerable morbidity and mortality, causing diseases such as pneumonia, bacteremia, meningitis, acute otitis media, and sinusitis. It is estimated that 20% of S. pneumoniae cases lead to bacteremia, and other manifestations such as meningitis, with a mortality rate close to 30% even with antibiotic treatment. S. pneumoniae is found in the nasopharynx of 11-76% of the population, averaging 40-50% for children and 20-30% for adults (Ghaffar et al., J. Infect. Dis. 18, 638-646, 1999).
Those most commonly at risk for pneumococcal infection are children between 6 months and 4 years of age and adults over 60 years of age. Virtually every child will experience pneumococcal otitis media before the age of 5 years. It is estimated that 25% of all community-acquired pneumonia is due to pneumococcus (1,000 per 100,000 inhabitants). Recently, epidemics of disease have reappeared in settings such as chronic care facilities, military camps, and day care centers, a situation not recognized since the pre-antibiotic era. S. pneumoniae remains a significant human pathogen because of the morbidity and mortality it causes in young children, the elderly and in immune-compromised patients.
Amongst the diagnostic methods of pneumococcal pneumonia, bronchoalveolar lavage (BAL) or transthoracic needle aspiration are considered to be reliable, but they are invasive and cannot be performed routinely.
Identification of the bacterium in blood culture provides a definite diagnosis and can serve as an indicator of disease severity. However, the positivity rate of blood cultures rarely exceeds 10% in CAP (Chalasani et al., Chest., 108, 932-936, 1995), and can be below 1% if blood samples are obtained during antimicrobial treatment (Grace et al., Clin Infect Dis., 32, 1651-1655, 2001). Diagnosis of pneumococcal pneumonia is hindered by the lack of a highly sensitive and specific ‘gold standard’ method. Culture of sputum and nasopharyngeal secretions is controversial due to respiratory tract carriage of pneumococci. The limitations of culture based, conventional S. pneumoniae diagnostic tests make definitive diagnosis difficult to establish. For example, the isolation of S. pneumoniae from blood, the recognized definitive test for the presence of S. pneumoniae may lack sensitivity, only giving positive results in 20-30% of adult cases of pneumococcal pneumonia and less than 10% of children's cases. Serologic assays for both antibody and antigen detection suffer from a lack of specificity and sensitivity, for example the recently introduced urine antigen test, Binax NOW®, while shown to be sensitive and specific for adults by some studies, is unable to distinguish between carriage and disease in children.
Attempts to develop accurate diagnosis and assays were made leading to an increase, in clinical practice, of the use of polymerase chain reaction (PCR) protocols to detect bacteria in blood samples. Commercial PCR procedures applied to blood samples, use conserved PCR targets for genes that are common to all bacteria. This is a promising strategy for pathogens like Staphylococcus aureus and Gram-negative enteric bacilli, but not for S. pneumoniae. It is difficult for PCR against common bacterial genes to distinguish between S. pneumoniae and alpha-haemolytic streptococci, as they are closely related (Innings et al., J Clin Microbiol. 43, 5983-5991, 2005 and Lehmann et al., Med Microbiol Immunol. 197, 313-324, 2008).
In addition, the misidentification of pneumococcus-like viridans Streptococci (P-LVS) as S. pneumoniae presents additional opportunities for misdiagnosis especially when attempted with non-sterile site specimens such as sputum. Identification of S. pneumoniae has typically been based on bile solubility, optochin sensitivity, and GenProbe ACCUPROBE® Pneumococcus identification test; but increasingly there have been reports of P-LVS isolated from clinical specimens, which may give positive or variable reactions in one or more of these standard pneumococcal tests. Among a subset of reported isolates of P-LVS, a newly recognized species, classified as S. pseudopneumoniae (Spseudo), has been described and characterized (Arbique et al., J. Clin. Microbiol. 42, 4686-4696, 2004). Spseudo organisms are bile solubility negative and resistant to optochin in the presence of 5% CO2, but are ACCUPROBE® positive (Arbique et al., J. Clin. Microbiol. 42, 4686-4696, 2004) and thus yield a false positive for S. pneumoniae infection. The appearance of these pneumococcus-like organisms has complicated identification and diagnosis even further, especially when non-sterile site respiratory specimens are used for making determinations.
U.S. Pat. No. 7,476,733 discloses a real-time PCR method for detection of the pneumococcal surface adhesion protein (psaA) gene. Patent application US 2010/0234245 provides methods for diagnosing an S. pneumoniae infection by analyzing a biological specimen from a subject to detect a broad variety of S. pneumoniae nucleic acids, such as S. pneumoniae lytA, ply, and psaA nucleic acids.
One of the major drawbacks of the methods described in the prior art is that they target the S. pneumoniae DNA. This drawback is due to the fact that S. pneumonia usually establishes an obligate asymptomatic association within the human nasopharyngeal cavity. This asymptomatic association leads to false positives when the pneumonia is caused by an organism different than S. pneumonia. Therefore, the need exists for diagnostic methods and assays allowing the detection of the presence and the activity of S. pneumoniae. 
The aim of the present invention is to provide a solution and to overcome the above mentioned disadvantage. An object of the invention is to propose a diagnostic method wherein the targeted nucleic acid is the RNA of S. pneumonia. The method, kit and device of the present invention are described hereafter and in the claims.